You can cut the runners off any time once they have rooted, in fact it's best at that stage so that the parent plant has a chance to build up its reserves for next year.
The newly rooted runners can be moved and transplanted at that stage if you want but it's always best to move the parent plants once they are dormant as root disturbance while they are in full growth will check their ability to build good cropping crowns.
So any time in the winter months or next spring just before the plants start to grow away again.
Sorry I can't suggest anything about chipmunks....something we don't have here...but with rabbits its either a fence that's all round the area and buried six inches below ground level or......a small piece of lead implanted just behind its ear.
An apple a day.....keeps me in work.